This is a competing renewal application of RO1 GM66047 (Studies of Protein Glycosylation). The broad objective of this project is to develop chemical tools for studies of protein glycosylation, the most prevalent and structurally diverse form of posttranslational modification. The next granting period is focused on two forms of Ser/Thr O-glycosylation for which chemical tools are needed: mucin-type O-glycosylation characterized by a conserved core N-acetylgalactosamine (GalNAc) residue, and O-GlcNAcylation in which Ser/Thr residues are modified with a single 2-N-acetylglucosamine (GlcNAc) residue. Changes in mucin-type O-glycoprotein expression have been associated with cancer. We hypothesize that prostate cancer biomarkers exist among this class of glycoproteins. Protein O-GlcNAcylation is a reversible signaling modification that is known to be critical for viability of embryos. We hypothesize that O-GlcNAcylation regulates proteins involved in human embryonic stem cell (hESC) differentiation and that differences in O-GlcNAcylation states contribute to the varied behavior of hESCs and induced pluripotent stem cells (iPSCs). We propose to develop new technologies for chemically-directed glycoproteomics (Aim 1) and to apply these tools to profile changes in mucin-type O-glycosylation associated with prostate cancer (Aim 2) and to profile O-GlcNAcylated proteins in differentiating hESC and iPSCs (Aim 3). The proposed glycoproteomics platform in Aim 1 combines two technologies developed in the last granting period: metabolic labeling of mucin-type O-glycans and O-GlcNAcylated proteins with azidosugars, and isotopic signature transfer and mass pattern prediction (IsoStamp) for chemically-directed mass spectrometry. IsoStamp exploits the perturbing effects of a dibrominated chemical tag on a peptide's mass envelope, which can be extracted from full-scan MS data sets using a computational algorithm we developed in-house. The method enables high- sensitivity detection of chemically tagged peptides from complex mixtures such as cell and tissue lysates. In addition to the use of metabolic labeling and IsoStamp, our glycoproteomics workflow includes glycosylation site-identification via ETD fragmentation, and quantitative comparative MS analysis with light and heavy IsoStamp tags. In Aim 2, these glycoproteomics tools will be used to identify mucin-type O-glycoproteins from human prostate cancer biopsy tissue as a function of Gleason grade, and for comparative studies with normal human prostate tissue. In Aim 3, we will probe changes in the O-GlcNAcylation states of cytosolic and nuclear proteins in human embryonic stem cells (hESCs) during neuronal differentiation. We will also perform a comparative analysis of O-GlcNAcylated proteins in hESCs and iPSCs.